Notes

Abstract:

Background: Traditional morphological and biological species concepts are difficult to apply to closely related,
asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic
species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been
extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more
accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal
agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase
gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species
boundaries were estimated using several approaches including those that incorporate uncertainty in gene
genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.
Results: Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage
sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported
at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus
brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2
and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the
human-mediated movement of citrus and associated pathogens out of SE Asia.
Conclusions: The number of Alternaria species identified as causing brown spot of citrus worldwide using
morphological criteria has been overestimated. Little support was found for most of these morphospecies using
quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for
understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the
movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that
allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual
species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing
citrus brown spot worldwide. Further research is needed to determine how these species were introduced
worldwide, how they differ phenotypically and how these species are maintained.
Keywords: Coalescent, Species delimitation, Species tree, Gene tree